RNA polymerase (RNAP) sensitively detects DNA damage as it performs one-dimensional scanning of the template strand, thus initiating transcription-coupled repair (TCR) or triggering apoptosis if the blockage persists. A detailed mechanistic understanding of the causes of transcription blockage and their outcomes should reveal novel modes and targets for selectively killing tumor cells, based upon differences in the genes they express compared to those of normal cells. The formation of long RNA/DNA hybrids (R-loops) during transcription can be a fundamental cause of RNAP arrest, and could produce a number of consequent deleterious effects in cells, including apoptosis. We predict that R-loop formation could be targeted to any transcribed sequence with high efficiency, either by co-transcriptional anchoring of nascent RNA to the DNA template (e.g., by "bivalent" oligonucleotides which can simultaneously form a triplex with DNA and a duplex with RNA) or by sequestration of the non-template strand by a sequence-specific peptide nucleic acid (PNA), a synthetic DNA mimic with superior DNA binding potential that is resistant to disruption by cellular enzymes. We propose a novel approach to selectively incapacitate a unique cell type with a distinguishable transcription profile, by targeting R-loop formation to a selected active gene. The combination of R-loop formation and arrested RNAP should also strongly block advancing replication forks to stifle proliferation, thus ensuring an even more robust lethal outcome. In fact, the transcription of this particular gene becomes "toxic" for the cell, regardles of its function and whether or not it is essential. In essence, we intend to make the very act of transcription lethal for the targeted cancer cells without affecting the normal cells. We will pursue the feasibility of this strategy;first, by testing the ability of various PNAs and anchorin oligonucleotides to induce R-loop formation, using in vitro transcription assays with T7 RNAP and RNAP II in HeLa cell nuclear extracts, combined with enzymological approaches and gel electrophoresis to characterize reaction products. Successful in vitro R-loop-inducing reagents will then be introduced into cells and their effects upon transcription, replication and cell lethaity will be monitored. In parallel, we will carry out studies to improve the efficiency of the deliveryof PNA to the target cells. We also propose to extend our studies of intrinsic transcription blockage by G-rich sequences and their biological implications. The results from the proposed studies will provide important insights into the regulation of gene expression and will contribute to the development of novel approaches in chemotherapy for cancer and human genetic disease.

Public Health Relevance

This project will explore a novel approach to achieve selective cell lethality in cancer therapy, in which the very act of transcription becomes toxic, as the nascent RNA product becomes anchored to the DNA template, thereby arresting the RNA polymerase (and blocking subsequent DNA replication) in a gene that is expressed in cells from a tumor but not in normal cells. The studies will also enhance our understanding of the roles of transcription in processing unusual DNA structures that have been implicated in cancer etiology and human hereditary disease.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
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Cancer Etiology Study Section (CE)
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Okano, Paul
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Stanford University
Schools of Arts and Sciences
United States
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Belotserkovskii, Boris P; Hanawalt, Philip C (2015) PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation. Mol Carcinog 54:1508-12
Belotserkovskii, Boris P; Neil, Alexander J; Saleh, Syed Shayon et al. (2013) Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks. Nucleic Acids Res 41:1817-28
Belotserkovskii, Boris P; Hanawalt, Philip C (2011) Anchoring nascent RNA to the DNA template could interfere with transcription. Biophys J 100:675-84
Belotserkovskii, Boris P; Liu, Richard; Tornaletti, Silvia et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences. Proc Natl Acad Sci U S A 107:12816-21
Belotserkovskii, Boris P; Liu, Richard; Hanawalt, Philip C (2009) Peptide nucleic acid (PNA) binding and its effect on in vitro transcription in friedreich's ataxia triplet repeats. Mol Carcinog 48:299-308
Hanawalt, Philip C (2008) Emerging links between premature ageing and defective DNA repair. Mech Ageing Dev 129:503-5
Belotserkovskii, Boris P; De Silva, Erandi; Tornaletti, Silvia et al. (2007) A triplex-forming sequence from the human c-MYC promoter interferes with DNA transcription. J Biol Chem 282:32433-41
Hsu, Pei-hsin; Hanawalt, Philip C; Nouspikel, Thierry (2007) Nucleotide excision repair phenotype of human acute myeloid leukemia cell lines at various stages of differentiation. Mutat Res 614:3-15
Cline, Susan D; Hanawalt, Philip C (2006) Topoisomerase deficiencies subtly enhance global genomic repair of ultraviolet-induced DNA damage in Saccharomyces cerevisiae. DNA Repair (Amst) 5:611-7
Nouspikel, Thierry; Hanawalt, Philip C (2006) Impaired nucleotide excision repair upon macrophage differentiation is corrected by E1 ubiquitin-activating enzyme. Proc Natl Acad Sci U S A 103:16188-93

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